The features of this PR primarily concerns bioinformaticians
microSALT now more aggressively checks the organism supplied
microSALT now uses the unfiltered organism name more readily in reports
This change was prompted by S. pseudomonas incorrectly identifying as Kleb(s)iella pseudomonas.
Primary function of PR
[X] Hotfix
[ ] Patch
[ ] Minor functionality improvement
[ ] New type of analysis
[ ] Backward-breaking functionality improvement
[ ] This change requires internal documents to be updated
[ ] This change requires another repository to be updated
Testing
microSALT analysis should be run on one of the misbehaving samples (ACC5746A8).
The log should warn about the exception, but both the Typing and QC report should report the correct organism (albeit the Typing report defaulting on about every data point since no pubMLST reference exists).
Test results
Both reports were successfully generated and contained the correct organism 'S. pseudomonas' instead of the previously incorrect 'Klebsiella pseudomonas' one.
Sign-offs
[X] Code reviewed by @sylvinite
[X] Code tested by @sylvinite
[x] Approved to run at Clinical-Genomics by @ingkebil
Description
The features of this PR primarily concerns bioinformaticians
This change was prompted by S. pseudomonas incorrectly identifying as Kleb(s)iella pseudomonas.
Primary function of PR
Testing
microSALT analysis should be run on one of the misbehaving samples (ACC5746A8). The log should warn about the exception, but both the Typing and QC report should report the correct organism (albeit the Typing report defaulting on about every data point since no pubMLST reference exists).
Test results
Both reports were successfully generated and contained the correct organism 'S. pseudomonas' instead of the previously incorrect 'Klebsiella pseudomonas' one.
Sign-offs